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Astrobiology, homochirality, and origins of life

Explore the fascinating connection between astrobiology, homochirality, and the origins of life. Discover the role of Nordic countries and Nordita in this field, with interests ranging from the peptide and RNA worlds to the Pencil Code and community efforts. Suitable for distributed systems.

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Astrobiology, homochirality, and origins of life

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  1. Astrobiology, homochirality, and origins of life • The four corner stones of astrobiology • Astrobiology in Nordic countries • Role of Nordita • Our current interests: • homochirality and origin of life • peptide world, RNA world • Pencil Code • Community effort • Suitable for distributed systems Int. J. Astrobio. 3, 209 (2004), 4, 75 (2005), Orig. Life Evol. Biosph. 35, 225 (2005), 35, 507 (2005) Astrobiology 7, 725 (2007)

  2. Topics at Nordic AB meetings Atmospheric escape Martian gullies Icelandic analogues Subglacial lakes Geological evolution Cyanobacteria Deep biosphere Extremophiles Deep biosphere Meteorites stardust RNA world Geochemistry astrochemistry Nucleotide Synthesis In space Deep biosph Ancient DNA, PNA, Early life evidence Climate, exoplanets Mars simulator Interstellar chem.

  3. Urey-Miller experiment (1953) Wait 1 week Reduced gases: H2, NH3, CH4, CO Result: NH2-CH2-COOH, etc 15 organic compounds 2% amino acids (11 different ones)

  4. From exoplanets toextremophiles Radial vel. Transits Direct microlensing

  5. Carbonic and organic carbon, CaCO3 versus (CH2O) n On Earth: Life 3.8 Gyrago Frozen/liquid water on Mars

  6. Time line First life planetesimals Sun ignites T0=1010 yr after Big Bang All gas gone Remaining dust settles 104 yr 106 yr 108 yr 109 yr

  7. From dust to planets Exoplanets Water delivery Habitable worlds Archaen world Volcanos, carbon cycle Impacts, panspermia Greenhouse effect Miller experiment Amino acids, chemistry Artificial life Origin of life RNA world, PNA world homochirality Early life Extremophiles Cyanobacteria Oxygen, methane evol. LUCA Astrobiology: the range of problems

  8. Onset of life • There is no good definition of life • replication (birth/death), evolution, metabolism • Protolife (simplistic): 2H2+CO2 (CH2O)+H2O • Ignores waste produced: CH4 ,H3C-COOH, or O2 • Ignores replication machinery • Hypothesis: primitive life is unavoidable • Several independent geneses of life on early Earth? • No serious competitors to carbon-based life

  9. Aminoacids in proteins: left-handedSugars in DNA and RNA: right-handed Is chirality: (i) prerequisite (ii) consequence of life? carboxyl group Louis Pasteur (1822-1895) animo group chlorophyll

  10. (from lecture of Antoine Weiss) Racemic mixture 6 Racemization dating method 5

  11. Origins of Homochirality

  12. Origin of life ~ origin of homochirality • Life requires homochirality • wrong enantiomer: stops polymerization • right and left do not cooperate • Dead cells racemize • Also: protolife may produce chirality • encymatic reactions keep system from equilibrium • as a result of polymerization • But: prebiotic soup was racemic!

  13. Producing enantiomeric excess (e.e.) • Life only develops in homochiral environment • Homochirality is then a prerequisite • However: no mechanism produces 100% e.e. • only minute partial excess possible (electroweak) • slightly bigger for large Z, goes like Z5 Cu (II) ions • Still need amplification mechanism • Frank (1953) model (plus extensions): nucleotides • Autocatalysis and enantiomeric cross inhibition • Plasson, Bersini, Commeyras (2004): peptides

  14. Chirality selection during polymerizationof the first replicating molecule? lipid world PNA world dual world RNA world achiral RNA DNA proteins RNA chiral Rasmussen et al (2003 Artif. Life9, 269-316) Isotactic polymer (same chirality) R Polymerization “waste” (enantiomeric cross-inhibition) L

  15. Exponential amplificationrecap of Frank-type model (Frank 1953) auto-catalysis alone kinetic equation exponential growth enantiomeric excess: catalyst

  16. Need also mutual antagonism(to siphon off the bad guys) add cross-inhibition kinetic equation unspecific antagonism

  17. Prebiotic experiments: nucleotides template-directed polymerization ~polymerase chain reaction (PCR) Serious difficulty: requires building blocks of the same chirality  Mononucleotides with wrong chirality terminate chain growth Joyce et al. (1984) ok poisoned poly (CD)  oligo (GD) (HPLC) guanine cytosine

  18. Contergan: was sold as racemic mixture Cures morning sickness during pregnancy causes misformations (abandoned in December 1961)

  19. Steps toward realism • Consider polymerization of nucleotides i.e. homochirality developed during RNA world autocatalysis requires longish polymers • Peptide world (new mechanism) no explicit autocatalysis required appears chemically feasible • Spatially extended systems independent origins at different locations on Earth

  20. (i) Polymerization model of Sandars Orig. Life Evol. Biosph. 33, 575-587 (2003) Reaction for left-handed monomers Loss term for each constituent

  21. 3 different classes of mechanisms • Autocatalysis and mutual antagonism- - Frank (1953) model - Grow both, and dump pairs - Has been applied to RNA world • crystal growth with stirring - larger crystals spawn more nucelation sites • constructive autocatalysis (see below) - has been applied to peptides

  22. Activation D  D*, L  L* Polymerization D+D DD, L+L  LL Epimerization DL  LL, LD  DD Depolymerization DD  D+D, LL  L+L Template-directed (PCR-like) Enantiomeric cross-inhibition Autocatalytic production of new mono-nucleotides ( but uncertain) RNA stability… (ii) RNA versus peptide worlds peptide world RNA world APED model (Plasson et al.)

  23. Net reactions

  24. Reduced APED model a one way round-about For nearly racemic state:

  25. (iii) Spatially extended model with Tuomas Multamäki, Int. J. Astrobio. 3, 209 (2004) Reaction-diffusion equation 1350 1349 Proto type: Fisher’s equation 1348 Propagating front solutions 1347 wave speed Spread of the black death

  26. 1D reduced model (reaction-diffusion equation) Propagation into racemic environment

  27. 2D model (reaction-diffusion equation) (X-Y)[1-(X-Y)2 /(X-Y)2] X

  28. Piecewise linear increase

  29. Piecewise linear increase Reduced equations add/subtract:

  30. Initial e.e. not related to final e.e.

  31. 3-D and effects of turbulence

  32. Where could this work? a) hydrothermal vents Braun & Libchaber (2003) b) Deep biosphere ideas about first Protocells Michael J. Russell (2006, Am. Sci. 94, 32-39)

  33. PencilCode • Started in Sept. 2001 with Wolfgang Dobler • High order (6th order in space, 3rd order in time) • Cache & memory efficient • MPI, can run PacxMPI (across countries!) • Maintained/developed by ~40 people (SVN) • Automatic validation (over night or any time) • Max resolution so far 10243 , 4096 procs • http://pencil-code.googlecode.com • Isotropic turbulence • MHD, passive scl, CR • Stratified layers • Convection, radiation • Shearing box • MRI, dust, interstellar • Self-gravity • Sphere embedded in box • Fully convective stars • geodynamo • Other applications • Homochirality • Spherical coordinates

  34. Conclusions • Astrobiology: need to be prepared… • Polymerization model: • Based on measurable processes • Reduction to accurate simplified model • Homochirality in space (earth, interstellar, etc) • Timescales 500 Myr; fossil evidence of spatially fragmented homochirality? • Pencil Code: just google for it • Detailed manual, …

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